# By using this file you agree to the legally binding terms of use found at # https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. # To request access to the AlphaFold 3 model parameters, follow the process set # out at https://github.com/google-deepmind/alphafold3. You may only use these if # received directly from Google. Use is subject to terms of use available at # https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. data_spkb23228 # _entry.id spkb23228 # loop_ _atom_type.symbol C N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Google DeepMind" 1 "Isomorphic Labs" 2 # _audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic _audit_conform.dict_name mmcif_ma.dic _audit_conform.dict_version 1.4.5 # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_smiles _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.093 ALA y ALANINE C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 ILE y ISOLEUCINE CC[C@H](C)[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C5 H11 N O2" 117.146 VAL y VALINE CC(C)[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" # _citation.book_publisher ? _citation.country UK _citation.id primary _citation.journal_full Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 0028-0836 _citation.journal_volume 630 _citation.page_first 493 _citation.page_last 500 _citation.pdbx_database_id_DOI 10.1038/s41586-024-07487-w _citation.pdbx_database_id_PubMed 38718835 _citation.title "Accurate structure prediction of biomolecular interactions with AlphaFold 3" _citation.year 2024 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary "Google DeepMind" 1 primary "Isomorphic Labs" 2 # _entity.id 1 _entity.pdbx_description . _entity.type polymer # _entity_poly.entity_id 1 _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 n MET 1 1 n LYS 2 1 n LYS 3 1 n ILE 4 1 n LEU 5 1 n ALA 6 1 n LEU 7 1 n LEU 8 1 n VAL 9 1 n ILE 10 1 n ALA 11 1 n PRO 12 1 n LEU 13 1 n LEU 14 1 n VAL 15 1 n SER 16 # _ma_data.content_type "model coordinates" _ma_data.id 1 _ma_data.name Model # _ma_model_list.data_id 1 _ma_model_list.model_group_id 1 _ma_model_list.model_group_name "AlphaFold-beta-20231127 (3.0.0 @ 2025-07-06 02:28:41)" _ma_model_list.model_id 1 _ma_model_list.model_name "Top ranked model" _ma_model_list.model_type "Ab initio model" _ma_model_list.ordinal_id 1 # loop_ _ma_protocol_step.method_type _ma_protocol_step.ordinal_id _ma_protocol_step.protocol_id _ma_protocol_step.step_id "coevolution MSA" 1 1 1 "template search" 2 1 2 modeling 3 1 3 # loop_ _ma_qa_metric.id _ma_qa_metric.mode _ma_qa_metric.name _ma_qa_metric.software_group_id _ma_qa_metric.type 1 global pLDDT 1 pLDDT 2 local pLDDT 1 pLDDT # _ma_qa_metric_global.metric_id 1 _ma_qa_metric_global.metric_value 95.68 _ma_qa_metric_global.model_id 1 _ma_qa_metric_global.ordinal_id 1 # loop_ _ma_qa_metric_local.label_asym_id _ma_qa_metric_local.label_comp_id _ma_qa_metric_local.label_seq_id _ma_qa_metric_local.metric_id _ma_qa_metric_local.metric_value _ma_qa_metric_local.model_id _ma_qa_metric_local.ordinal_id A MET 1 2 92.12 1 1 A LYS 2 2 92.10 1 2 A LYS 3 2 94.06 1 3 A ILE 4 2 97.13 1 4 A LEU 5 2 95.80 1 5 A ALA 6 2 98.22 1 6 A LEU 7 2 96.93 1 7 A LEU 8 2 97.16 1 8 A VAL 9 2 97.96 1 9 A ILE 10 2 97.45 1 10 A ALA 11 2 98.21 1 11 A PRO 12 2 98.11 1 12 A LEU 13 2 96.53 1 13 A LEU 14 2 95.69 1 14 A VAL 15 2 96.61 1 15 A SER 16 2 89.21 1 16 # _ma_software_group.group_id 1 _ma_software_group.ordinal_id 1 _ma_software_group.software_id 1 # _ma_target_entity.data_id 1 _ma_target_entity.entity_id 1 _ma_target_entity.origin . # _ma_target_entity_instance.asym_id A _ma_target_entity_instance.details . _ma_target_entity_instance.entity_id 1 # loop_ _pdbx_data_usage.details _pdbx_data_usage.id _pdbx_data_usage.type _pdbx_data_usage.url ;Non-commercial use only, by using this file you agree to the terms of use found at https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. To request access to the AlphaFold 3 model parameters, follow the process set out at https://github.com/google-deepmind/alphafold3. You may only use these if received directly from Google. Use is subject to terms of use available at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. ; 1 license https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md ;AlphaFold 3 and its output are not intended for, have not been validated for, and are not approved for clinical use. They are provided "as-is" without any warranty of any kind, whether expressed or implied. No warranty is given that use shall not infringe the rights of any third party. ; 2 disclaimer ? # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.hetero _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id A 1 1 n MET . 1 A 1 A 2 1 n LYS . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n SER . 16 A 16 # _software.classification other _software.date ? _software.description "Structure prediction" _software.name AlphaFold _software.pdbx_ordinal 1 _software.type package _software.version "AlphaFold-beta-20231127 (9ceee3b5f7825b611ab42eaad843248507ced2da1e745fa3b3d93c6c4ad3ca74)" # _struct_asym.entity_id 1 _struct_asym.id A # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . MET A 1 1 ? 10.491 11.070 2.959 1.00 96.64 1 A 1 ATOM 2 C CA . MET A 1 1 ? 9.531 10.737 1.882 1.00 97.25 1 A 1 ATOM 3 C C . MET A 1 1 ? 8.295 10.065 2.479 1.00 97.27 1 A 1 ATOM 4 O O . MET A 1 1 ? 8.368 8.938 2.950 1.00 96.32 1 A 1 ATOM 5 C CB . MET A 1 1 ? 10.186 9.795 0.876 1.00 95.42 1 A 1 ATOM 6 C CG . MET A 1 1 ? 11.360 10.458 0.180 1.00 89.78 1 A 1 ATOM 7 S SD . MET A 1 1 ? 12.235 9.327 -0.896 1.00 86.53 1 A 1 ATOM 8 C CE . MET A 1 1 ? 13.576 10.373 -1.426 1.00 77.73 1 A 1 ATOM 9 N N . LYS A 1 2 ? 7.163 10.769 2.462 1.00 97.15 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 5.913 10.262 3.034 1.00 97.76 2 A 1 ATOM 11 C C . LYS A 1 2 ? 5.086 9.486 2.010 1.00 97.98 2 A 1 ATOM 12 O O . LYS A 1 2 ? 4.240 8.680 2.385 1.00 97.23 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 5.098 11.437 3.575 1.00 96.92 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 5.775 12.140 4.740 1.00 91.81 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 5.427 11.479 6.057 1.00 89.93 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 5.974 12.266 7.229 1.00 83.47 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 5.633 11.615 8.508 1.00 76.68 2 A 1 ATOM 18 N N . LYS A 1 3 ? 5.316 9.736 0.738 1.00 98.12 3 A 1 ATOM 19 C CA . LYS A 1 3 ? 4.566 9.067 -0.328 1.00 98.33 3 A 1 ATOM 20 C C . LYS A 1 3 ? 4.789 7.556 -0.300 1.00 98.36 3 A 1 ATOM 21 O O . LYS A 1 3 ? 3.875 6.786 -0.582 1.00 97.80 3 A 1 ATOM 22 C CB . LYS A 1 3 ? 4.959 9.651 -1.687 1.00 98.05 3 A 1 ATOM 23 C CG . LYS A 1 3 ? 6.399 9.370 -2.073 1.00 95.17 3 A 1 ATOM 24 C CD . LYS A 1 3 ? 6.539 9.314 -3.582 1.00 92.13 3 A 1 ATOM 25 C CE . LYS A 1 3 ? 7.850 8.674 -3.990 1.00 87.71 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? 7.851 8.350 -5.436 1.00 80.91 3 A 1 ATOM 27 N N . ILE A 1 4 ? 5.986 7.138 0.047 1.00 98.05 4 A 1 ATOM 28 C CA . ILE A 1 4 ? 6.315 5.719 0.112 1.00 98.05 4 A 1 ATOM 29 C C . ILE A 1 4 ? 5.599 5.054 1.279 1.00 98.07 4 A 1 ATOM 30 O O . ILE A 1 4 ? 5.076 3.949 1.158 1.00 97.54 4 A 1 ATOM 31 C CB . ILE A 1 4 ? 7.835 5.522 0.241 1.00 98.12 4 A 1 ATOM 32 C CG1 . ILE A 1 4 ? 8.562 6.107 -0.968 1.00 96.93 4 A 1 ATOM 33 C CG2 . ILE A 1 4 ? 8.162 4.032 0.350 1.00 96.32 4 A 1 ATOM 34 C CD1 . ILE A 1 4 ? 9.945 6.579 -0.624 1.00 93.93 4 A 1 ATOM 35 N N . LEU A 1 5 ? 5.570 5.721 2.402 1.00 98.02 5 A 1 ATOM 36 C CA . LEU A 1 5 ? 4.905 5.195 3.591 1.00 97.87 5 A 1 ATOM 37 C C . LEU A 1 5 ? 3.400 5.098 3.366 1.00 97.98 5 A 1 ATOM 38 O O . LEU A 1 5 ? 2.762 4.137 3.792 1.00 97.84 5 A 1 ATOM 39 C CB . LEU A 1 5 ? 5.197 6.099 4.785 1.00 97.65 5 A 1 ATOM 40 C CG . LEU A 1 5 ? 4.697 5.535 6.112 1.00 93.66 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? 5.502 4.305 6.509 1.00 91.55 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? 4.789 6.586 7.207 1.00 91.84 5 A 1 ATOM 43 N N . ALA A 1 6 ? 2.832 6.084 2.712 1.00 98.35 6 A 1 ATOM 44 C CA . ALA A 1 6 ? 1.400 6.113 2.428 1.00 98.28 6 A 1 ATOM 45 C C . ALA A 1 6 ? 1.006 4.965 1.503 1.00 98.39 6 A 1 ATOM 46 O O . ALA A 1 6 ? -0.005 4.303 1.712 1.00 98.04 6 A 1 ATOM 47 C CB . ALA A 1 6 ? 1.034 7.446 1.791 1.00 98.05 6 A 1 ATOM 48 N N . LEU A 1 7 ? 1.819 4.725 0.483 1.00 98.37 7 A 1 ATOM 49 C CA . LEU A 1 7 ? 1.551 3.653 -0.474 1.00 98.46 7 A 1 ATOM 50 C C . LEU A 1 7 ? 1.696 2.289 0.190 1.00 98.61 7 A 1 ATOM 51 O O . LEU A 1 7 ? 0.981 1.349 -0.149 1.00 98.41 7 A 1 ATOM 52 C CB . LEU A 1 7 ? 2.525 3.769 -1.647 1.00 98.29 7 A 1 ATOM 53 C CG . LEU A 1 7 ? 2.162 4.883 -2.623 1.00 95.86 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? 3.386 5.324 -3.412 1.00 93.39 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? 1.077 4.407 -3.581 1.00 94.06 7 A 1 ATOM 56 N N . LEU A 1 8 ? 2.603 2.185 1.124 1.00 98.54 8 A 1 ATOM 57 C CA . LEU A 1 8 ? 2.848 0.934 1.838 1.00 98.57 8 A 1 ATOM 58 C C . LEU A 1 8 ? 1.689 0.590 2.765 1.00 98.67 8 A 1 ATOM 59 O O . LEU A 1 8 ? 1.584 -0.529 3.250 1.00 98.49 8 A 1 ATOM 60 C CB . LEU A 1 8 ? 4.150 1.053 2.630 1.00 98.42 8 A 1 ATOM 61 C CG . LEU A 1 8 ? 4.978 -0.230 2.629 1.00 96.09 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? 6.462 0.097 2.709 1.00 93.78 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? 4.592 -1.126 3.793 1.00 94.69 8 A 1 ATOM 64 N N . VAL A 1 9 ? 0.821 1.544 3.014 1.00 98.57 9 A 1 ATOM 65 C CA . VAL A 1 9 ? -0.337 1.328 3.879 1.00 98.54 9 A 1 ATOM 66 C C . VAL A 1 9 ? -1.607 1.119 3.057 1.00 98.63 9 A 1 ATOM 67 O O . VAL A 1 9 ? -2.498 0.367 3.452 1.00 98.37 9 A 1 ATOM 68 C CB . VAL A 1 9 ? -0.526 2.520 4.829 1.00 98.19 9 A 1 ATOM 69 C CG1 . VAL A 1 9 ? -1.732 2.306 5.725 1.00 96.63 9 A 1 ATOM 70 C CG2 . VAL A 1 9 ? 0.718 2.718 5.677 1.00 96.79 9 A 1 ATOM 71 N N . ILE A 1 10 ? -1.693 1.789 1.925 1.00 98.54 10 A 1 ATOM 72 C CA . ILE A 1 10 ? -2.864 1.693 1.058 1.00 98.49 10 A 1 ATOM 73 C C . ILE A 1 10 ? -2.917 0.347 0.346 1.00 98.58 10 A 1 ATOM 74 O O . ILE A 1 10 ? -3.975 -0.267 0.237 1.00 98.35 10 A 1 ATOM 75 C CB . ILE A 1 10 ? -2.867 2.835 0.030 1.00 98.20 10 A 1 ATOM 76 C CG1 . ILE A 1 10 ? -2.911 4.193 0.750 1.00 96.43 10 A 1 ATOM 77 C CG2 . ILE A 1 10 ? -4.062 2.701 -0.911 1.00 96.16 10 A 1 ATOM 78 C CD1 . ILE A 1 10 ? -4.149 4.373 1.603 1.00 94.83 10 A 1 ATOM 79 N N . ALA A 1 11 ? -1.778 -0.105 -0.155 1.00 98.41 11 A 1 ATOM 80 C CA . ALA A 1 11 ? -1.709 -1.375 -0.876 1.00 98.36 11 A 1 ATOM 81 C C . ALA A 1 11 ? -2.115 -2.557 0.008 1.00 98.44 11 A 1 ATOM 82 O O . ALA A 1 11 ? -3.025 -3.308 -0.341 1.00 97.88 11 A 1 ATOM 83 C CB . ALA A 1 11 ? -0.312 -1.572 -1.453 1.00 97.97 11 A 1 ATOM 84 N N . PRO A 1 12 ? -1.459 -2.747 1.145 1.00 98.56 12 A 1 ATOM 85 C CA . PRO A 1 12 ? -1.788 -3.859 2.049 1.00 98.42 12 A 1 ATOM 86 C C . PRO A 1 12 ? -3.168 -3.719 2.673 1.00 98.50 12 A 1 ATOM 87 O O . PRO A 1 12 ? -3.786 -4.711 3.046 1.00 97.99 12 A 1 ATOM 88 C CB . PRO A 1 12 ? -0.698 -3.779 3.120 1.00 97.92 12 A 1 ATOM 89 C CG . PRO A 1 12 ? -0.194 -2.388 3.060 1.00 97.08 12 A 1 ATOM 90 C CD . PRO A 1 12 ? -0.325 -1.966 1.623 1.00 98.31 12 A 1 ATOM 91 N N . LEU A 1 13 ? -3.654 -2.517 2.789 1.00 98.23 13 A 1 ATOM 92 C CA . LEU A 1 13 ? -4.975 -2.263 3.365 1.00 98.26 13 A 1 ATOM 93 C C . LEU A 1 13 ? -6.063 -2.860 2.486 1.00 98.38 13 A 1 ATOM 94 O O . LEU A 1 13 ? -7.066 -3.365 2.987 1.00 97.55 13 A 1 ATOM 95 C CB . LEU A 1 13 ? -5.198 -0.756 3.507 1.00 97.93 13 A 1 ATOM 96 C CG . LEU A 1 13 ? -6.388 -0.418 4.397 1.00 95.67 13 A 1 ATOM 97 C CD1 . LEU A 1 13 ? -5.910 0.219 5.695 1.00 93.40 13 A 1 ATOM 98 C CD2 . LEU A 1 13 ? -7.343 0.522 3.682 1.00 92.81 13 A 1 ATOM 99 N N . LEU A 1 14 ? -5.870 -2.810 1.177 1.00 97.77 14 A 1 ATOM 100 C CA . LEU A 1 14 ? -6.842 -3.349 0.228 1.00 97.76 14 A 1 ATOM 101 C C . LEU A 1 14 ? -6.874 -4.870 0.295 1.00 97.85 14 A 1 ATOM 102 O O . LEU A 1 14 ? -7.929 -5.484 0.144 1.00 97.00 14 A 1 ATOM 103 C CB . LEU A 1 14 ? -6.487 -2.899 -1.188 1.00 97.40 14 A 1 ATOM 104 C CG . LEU A 1 14 ? -7.564 -3.225 -2.216 1.00 95.08 14 A 1 ATOM 105 C CD1 . LEU A 1 14 ? -8.731 -2.257 -2.078 1.00 91.72 14 A 1 ATOM 106 C CD2 . LEU A 1 14 ? -6.997 -3.153 -3.625 1.00 90.98 14 A 1 ATOM 107 N N . VAL A 1 15 ? -5.738 -5.482 0.503 1.00 98.08 15 A 1 ATOM 108 C CA . VAL A 1 15 ? -5.628 -6.939 0.590 1.00 97.95 15 A 1 ATOM 109 C C . VAL A 1 15 ? -6.333 -7.464 1.838 1.00 98.01 15 A 1 ATOM 110 O O . VAL A 1 15 ? -6.929 -8.543 1.819 1.00 97.25 15 A 1 ATOM 111 C CB . VAL A 1 15 ? -4.156 -7.364 0.607 1.00 97.19 15 A 1 ATOM 112 C CG1 . VAL A 1 15 ? -4.040 -8.876 0.662 1.00 93.47 15 A 1 ATOM 113 C CG2 . VAL A 1 15 ? -3.433 -6.829 -0.614 1.00 94.29 15 A 1 ATOM 114 N N . SER A 1 16 ? -6.266 -6.707 2.895 1.00 95.80 16 A 1 ATOM 115 C CA . SER A 1 16 ? -6.883 -7.103 4.165 1.00 94.27 16 A 1 ATOM 116 C C . SER A 1 16 ? -8.246 -6.452 4.345 1.00 91.41 16 A 1 ATOM 117 O O . SER A 1 16 ? -8.374 -5.522 5.160 1.00 85.59 16 A 1 ATOM 118 C CB . SER A 1 16 ? -5.976 -6.731 5.329 1.00 91.19 16 A 1 ATOM 119 O OG . SER A 1 16 ? -4.720 -7.351 5.212 1.00 82.58 16 A 1 ATOM 120 O OXT . SER A 1 16 ? -9.199 -6.877 3.670 1.00 83.63 16 A 1 #